Will taking Spanish 3 but not taking Spanish 1 and 2 count as 3 levels of foreign language?

Yes you absolutely can take Arabic 1 and Arabic 2, and have completed more than if you just took Middle School 1+2 and a year in HS. In addition, Arabic is much sought after so it’d give you an edge in admissions.
However, be aware that the pace is brutal (obviously, you cover roughly 1 month of HS language in 1 week!) and Arabic is one of the hardest languages in the world, you’ll need to schedule about 3 hours each day just for Arabic homework. If you already know some Arabic (ie., neighbors, friends, family speak it), it’d definitely give you an advantage.